In silico microarray probe design for diagnosis of multiple pathogens.

ABSTRACT:

Background

With multiple strains of various pathogens being sequenced, it is necessary to develop high-throughput methods that can simultaneously process multiple bacterial or viral genomes to find common fingerprints as well as fingerprints that are unique to each individual genome. We present algorithmic enhancements to an existing single-genome pipeline that allows for efficient design of microarray probes common to groups of target genomes. The enhanced pipeline takes advantage of the similarities in the input genomes to narrow the search to short, nonredundant regions of the target genomes and, thereby, significantly reduces the computation time. The pipeline also computes a three-state hybridization matrix, which gives the expected hybridization of each probe with each target

SUBMITTER: Vijaya Satya R 

PROVIDER: S-EPMC2596143 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature